Climate change will have a greater impact on the severity of flash floods, since precipitation intensity is expected to increase, even in areas where a reduction of precipitation is possible. This change in climate is expected to increase flood wave speed and its flood wave area extent. A case study of a small basin in the island of Crete was conducted to examine this effect, following the calibration and validation of the flow hydrograph of a flash flood event, in order to achieve model verification with the post-flood data. It was found that the most important parameters that affect the timing and magnitude of the peak discharge are the storage coefficient, the impervious rate and the curve number, as well as the time of concentration. Rainfall distribution was examined in different time intervals in order to study the effect of the intensity of precipitation on the peak hydrograph. From the precipitation records and according to the size of the watershed, the time step of the precipitation in the simulation model is recommended to be less than an hour. In other areas around the basin of interest, severe storms known as Medicanes that pass over Crete can produce higher precipitation in shorter time intervals. The impact of climate change scenarios results in an increase on the peak discharge by creating precipitation of higher intensity. Furthermore, the intensification of precipitation due to climate change results in higher flood depths and flooded area extent, as well as wave velocities.